BN1864 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.0923e-05 1.1631e-04
Layer 3 1.1737e-05 2.4485e-04
Layer 2 4.4019e-05 1.2128e-02
Layer 5 1.3331e-04 4.3142e-04
Layer 6 3.9795e-04 2.2271e-03
Layer 1 4.2625e-01 3.2599e-01
WM 9.9781e-01 4.5327e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
PPP2R1A Expression Distribution
Gene Specificity Score (GSS)
PPP2R1A GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
PPP2R1A Layer 4 3.3945 0.8668
RTN1 Layer 4 3.9375 0.8656
GDI1 Layer 4 3.4316 0.8641
SYN1 Layer 4 4.1562 0.8616
FKBP8 Layer 5 3.1113 0.8615
YWHAG Layer 5 3.4980 0.8588
NEFL Layer 5 3.5977 0.8573
PRKAR1B Layer 5 3.3711 0.8572
PKM Layer 4 3.7324 0.8571
SNRPN Layer 5 3.5508 0.8558
ENO2 Layer 4 4.2734 0.8555
GPI Layer 5 3.6836 0.8554
NDRG4 Layer 4 3.7070 0.8554
MORF4L1 Layer 4 3.5586 0.8553
RTN3 Layer 4 3.7246 0.8546
APBB1 Layer 4 3.5586 0.8540
FAIM2 Layer 4 3.9043 0.8538
NGRN Layer 5 3.4902 0.8537
LMO4 Layer 4 3.7402 0.8537
GRIN1 Layer 4 3.9551 0.8535
SPTBN1 Layer 5 3.2793 0.8534
KLC1 Layer 5 3.4160 0.8534
CFL1 Layer 5 3.4688 0.8533
SARAF Layer 4 3.3008 0.8520
STXBP1 Layer 4 3.8457 0.8520
SPTAN1 Layer 5 3.2578 0.8518
ARL6IP1 Layer 4 3.4375 0.8513
DNM1 Layer 5 3.5742 0.8506
OAZ1 Layer 4 3.5430 0.8505
KIF1A Layer 4 3.4238 0.8503
STMN1 Layer 5 3.8125 0.8503
PPIA Layer 5 3.2090 0.8499
APP Layer 5 3.7070 0.8498
SERINC1 Layer 4 3.1875 0.8497
DPYSL2 Layer 5 3.3359 0.8495
CLSTN1 Layer 4 3.9707 0.8494
ATP5F1B Layer 4 3.7715 0.8482
MAPK8IP2 Layer 4 4.1445 0.8478
TLE5 Layer 4 3.3574 0.8471
ATP6V0C Layer 5 3.4531 0.8467
SNCB Layer 4 3.5742 0.8464
UCHL1 Layer 5 3.4902 0.8463
TPI1 Layer 4 3.4316 0.8461
YWHAH Layer 4 3.4316 0.8456
SLC22A17 Layer 4 3.5293 0.8453
FBXL16 Layer 4 3.1797 0.8449
YWHAZ Layer 4 3.5430 0.8448
TSC22D1 Layer 4 3.4980 0.8447
PREPL Layer 5 3.4238 0.8443
MTCH1 Layer 5 3.4688 0.8442

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1864
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1864_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1864/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1864/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1864/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1864/report/PD/BN1864_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1864/report/PD/BN1864_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 09:05:58
  • Number of Processes: 10
  • Spending Time: 0h 3m